The efficient management of water resources depends on knowledge of the flows of the entire hydrographic basin. However, in most cases, basins have an insufficient monitoring network and flow measurement system, which can compromise the application of the grant instrument and cause damage to the environment and users. Therefore, it is necessary to develop hydrological models that provide information on the minimum flows in all water courses of the planning unit. Thus, this study aimed to propose a method to regionalize flows in areas with limited monitoring using hydrological data and geoprocessing tools. The Ivinhema River Basin, located in Mato Grosso do Sul State, Brazil, was adopted as the study area. The models were developed based on the correlation of physical and environmental variables, which was evaluated by the relative error and the Nash–Sutcliffe efficiency coefficient. Finally, the flow Q95 was spatialized, generating an accumulated flow map with the application of the selected model, and the corresponding Q95 was obtained for each stretch of the watercourse. The developed method provides relevant results and can be applied to various hydrographic basins.